Dear Amber experts,
I am simulating bilayer sistem in water.
I break my longer simulation period into smaller fractions where by each contain 1000 frames.
At first I reimage the system so that all the waters are in the box using below code:
trajin ../betaM_lyo_md02_0900.mdcrd.gz
trajout betaM_lyo_md02_0900.mdcrd mdcrd
center :1-256
image center familiar
the output of this run is as below.
DDM DDM DDM DDM DDM DDM DDM DDM DDM DDM
...
DDM DDM DDM DDM DDM DDM WAT WAT WAT WAT
WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
...
WAT WAT WAT WAT WAT WAT WAT WAT
Scanning Box
Successfully completed readParm.
PTRAJ: Processing input file...
Input is from standard input
PTRAJ: trajin ../betaM_lyo_md02_0900.mdcrd.gz
PTRAJ: trajout betaM_lyo_md02_0900.mdcrd mdcrd
PTRAJ: center :1-256
Mask [:1-256] represents 20736 atoms
PTRAJ: image center familiar
Mask [*] represents 23832 atoms
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 999 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (../betaM_lyo_md02_0900.mdcrd.gz) is an AMBER trajectory (with box info) with 999 sets
OUTPUT COORDINATE FILE
File (betaM_lyo_md02_0900.mdcrd) is an AMBER trajectory (with box info)
ACTIONS
1> CENTER to box center via center of geometry, atom selection follows :1-256
7> IMAGE familiar by molecule to box center using the center of mass, atom selection * (All atoms are selected)
IMAGE familiar, center is at box center
Processing AMBER trajectory file ../betaM_lyo_md02_0900.mdcrd.gz
Set 1 .................................................
Set 50 .................................................
Set 100 .................................................
Set 150 .................................................
Set 200 .................................................
Set 250 .................................................
Set 300 .....................
PTRAJ: Successfully read in 321 sets and processed 321 sets.
Dumping accumulated results (if any)
Actually it supposed to read 1000 frames, but it reads only 321 frames.
When I check the mdcrd file for any characters such as (*) .. I can't find any thing like this.
In one nanosecond simulatiojnn I have 10 files with each 1000 frames.
But some files are not shwoing any message like this in output file, but some are showing message like this.
I need help to overcome this problem.
I also done simulation again and again few times.
'But the results are still the same.
Any expert can help me?
I really appreciate your help.
Thank you.
Vijay
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Received on Sun Dec 02 2007 - 06:07:17 PST
